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Yao M, Oduro PK, Akintibu AM, Yan H. Modulation of the vitamin D receptor by traditional Chinese medicines and bioactive compounds: potential therapeutic applications in VDR-dependent diseases. Front Pharmacol 2024; 15:1298181. [PMID: 38318147 PMCID: PMC10839104 DOI: 10.3389/fphar.2024.1298181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
The Vitamin D receptor (VDR) is a crucial nuclear receptor that plays a vital role in various physiological functions. To a larger extent, the genomic effects of VDR maintain general wellbeing, and its modulation holds implications for multiple diseases. Current evidence regarding using vitamin D or its synthetic analogs to treat non-communicable diseases is insufficient, though observational studies suggest potential benefits. Traditional Chinese medicines (TCMs) and bioactive compounds derived from natural sources have garnered increasing attention. Interestingly, TCM formulae and TCM-derived bioactive compounds have shown promise in modulating VDR activities. This review explores the intriguing potential of TCM and bioactive compounds in modulating VDR activity. We first emphasize the latest information on the genetic expression, function, and structure of VDR, providing a comprehensive understanding of this crucial receptor. Following this, we review several TCM formulae and herbs known to influence VDR alongside the mechanisms underpinning their action. Similarly, we also discuss TCM-based bioactive compounds that target VDR, offering insights into their roles and modes of action.
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Affiliation(s)
- Minghe Yao
- Henan University of Chinese Medicine, Zhengzhou, China
- Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Zhengzhou, China
| | - Patrick Kwabena Oduro
- Jacobs School of Medicine and Biomedical Sciences, The State University of New York, University at Buffalo, Buffalo, NY, United States
| | - Ayomide M. Akintibu
- School of Community Health and Policy, Morgan State University, Baltimore, MD, United States
| | - Haifeng Yan
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
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2
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Structural overview and perspectives of the nuclear receptors, a major family as the direct targets for small-molecule drugs. Acta Biochim Biophys Sin (Shanghai) 2021; 54:12-24. [PMID: 35130630 PMCID: PMC9909358 DOI: 10.3724/abbs.2021001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The nuclear receptors (NRs) are an evolutionarily related family of transcription factors, which share certain common structural characteristics and regulate the expressions of various genes by recognizing different response elements. NRs play important roles in cell differentiation, proliferation, survival and apoptosis, rendering them indispensable in many physiological activities including growth and metabolism. As a result, dysfunctions of NRs are closely related to a variety of diseases, such as diabetes, obesity, infertility, inflammation, the Alzheimer's disease, cardiovascular diseases, prostate and breast cancers. Meanwhile, small-molecule drugs directly targeting NRs have been widely used in the treatment of above diseases. Here we summarize recent progress in the structural biology studies of NR family proteins. Compared with the dozens of structures of isolated DNA-binding domains (DBDs) and the striking more than a thousand of structures of isolated ligand-binding domains (LBDs) accumulated in the Protein Data Bank (PDB) over thirty years, by now there are only a small number of multi-domain NR complex structures, which reveal the integration of different NR domains capable of the allosteric signal transduction, or the detailed interactions between NR and various coregulator proteins. On the other hand, the structural information about several orphan NRs is still totally unavailable, hindering the further understanding of their functions. The fast development of new technologies in structural biology will certainly help us gain more comprehensive information of NR structures, inspiring the discovery of novel NR-targeting drugs with a new binding site beyond the classic LBD pockets and/or a new mechanism of action.
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3
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Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ. In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic Acids Res 2018; 46:8385-8403. [PMID: 30102401 PMCID: PMC6144799 DOI: 10.1093/nar/gky692] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
The constitutive androstane receptor (CAR; NR1I3) is a nuclear receptor orchestrating complex roles in cell and systems biology. Species differences in CAR's effector pathways remain poorly understood, including its role in regulating liver tumor promotion. We developed transgenic mouse models to assess genome-wide binding of mouse and human CAR, following receptor activation in liver with direct ligands and with phenobarbital, an indirect CAR activator. Genomic interaction profiles were integrated with transcriptional and biological pathway analyses. Newly identified CAR target genes included Gdf15 and Foxo3, important regulators of the carcinogenic process. Approximately 1000 genes exhibited differential binding interactions between mouse and human CAR, including the proto-oncogenes, Myc and Ikbke, which demonstrated preferential binding by mouse CAR as well as mouse CAR-selective transcriptional enhancement. The ChIP-exo analyses also identified distinct binding motifs for the respective mouse and human receptors. Together, the results provide new insights into the important roles that CAR contributes as a key modulator of numerous signaling pathways in mammalian organisms, presenting a genomic context that specifies species variation in biological processes under CAR's control, including liver cell proliferation and tumor promotion.
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Affiliation(s)
- Ben Niu
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Denise M Coslo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alain R Bataille
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Curtis J Omiecinski
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling. Curr Top Dev Biol 2017; 125:1-38. [DOI: 10.1016/bs.ctdb.2017.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Kojetin DJ, Matta-Camacho E, Hughes TS, Srinivasan S, Nwachukwu JC, Cavett V, Nowak J, Chalmers MJ, Marciano DP, Kamenecka TM, Shulman AI, Rance M, Griffin PR, Bruning JB, Nettles KW. Structural mechanism for signal transduction in RXR nuclear receptor heterodimers. Nat Commun 2015; 6:8013. [PMID: 26289479 PMCID: PMC4547401 DOI: 10.1038/ncomms9013] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/06/2015] [Indexed: 12/14/2022] Open
Abstract
A subset of nuclear receptors (NRs) function as obligate heterodimers with retinoid X receptor (RXR), allowing integration of ligand-dependent signals across the dimer interface via an unknown structural mechanism. Using nuclear magnetic resonance (NMR) spectroscopy, x-ray crystallography and hydrogen/deuterium exchange (HDX) mass spectrometry, here we show an allosteric mechanism through which RXR co-operates with a permissive dimer partner, peroxisome proliferator-activated receptor (PPAR)-γ, while rendered generally unresponsive by a non-permissive dimer partner, thyroid hormone (TR) receptor. Amino acid residues that mediate this allosteric mechanism comprise an evolutionarily conserved network discovered by statistical coupling analysis (SCA). This SCA network acts as a signalling rheostat to integrate signals between dimer partners, ligands and coregulator-binding sites, thereby affecting signal transmission in RXR heterodimers. These findings define rules guiding how NRs integrate two ligand-dependent signalling pathways into RXR heterodimer-specific responses. Some nuclear receptors dimerize with retinoid X receptor to allow ligand-dependent signalling. Here, Kojetin et al. use structural and biophysical techniques to identify structural changes that guide these complex signalling networks.
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Affiliation(s)
- Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Edna Matta-Camacho
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Travis S Hughes
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Valerie Cavett
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Michael J Chalmers
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - David P Marciano
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Andrew I Shulman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - John B Bruning
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
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Moras D, Billas IML, Rochel N, Klaholz BP. Structure-function relationships in nuclear receptors: the facts. Trends Biochem Sci 2015; 40:287-90. [PMID: 25899756 DOI: 10.1016/j.tibs.2015.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Dino Moras
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.
| | - Isabelle M L Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Natacha Rochel
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
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Fattori J, Indolfo NDC, Campos JCLDO, Videira NB, Bridi AV, Doratioto TR, Assis MAD, Figueira ACM. Investigation of Interactions between DNA and Nuclear Receptors: A Review of the Most Used Methods. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juliana Fattori
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Nathalia de Carvalho Indolfo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | | | - Natália Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Aline Villanova Bridi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Tábata Renée Doratioto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Michelle Alexandrino de Assis
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), P.O. Box 6192, Campinas-SP, Brazil
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Hughes TS, Giri PK, de Vera IMS, Marciano DP, Kuruvilla DS, Shin Y, Blayo AL, Kamenecka TM, Burris TP, Griffin PR, Kojetin DJ. An alternate binding site for PPARγ ligands. Nat Commun 2014; 5:3571. [PMID: 24705063 PMCID: PMC4070320 DOI: 10.1038/ncomms4571] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 03/06/2014] [Indexed: 12/18/2022] Open
Abstract
PPARγ is a target for insulin-sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands.
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Affiliation(s)
- Travis S Hughes
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Pankaj Kumar Giri
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Ian Mitchelle S de Vera
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - David P Marciano
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Dana S Kuruvilla
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Youseung Shin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Anne-Laure Blayo
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Thomas P Burris
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, USA
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9
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Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α. Nat Chem Biol 2013; 9:326-32. [PMID: 23524984 PMCID: PMC3631275 DOI: 10.1038/nchembio.1214] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/22/2013] [Indexed: 11/24/2022]
Abstract
Ligand-binding dynamics control allosteric signaling through the estrogen receptor-α (ERα), but the biological consequences of such dynamic binding orientations are unknown. Here, we compare a set of ER ligands having dynamic binding orientation (dynamic ligands) with a control set of isomers that are constrained to bind in a single orientation (constrained ligands). Proliferation of breast cancer cells directed by constrained ligands is associated with DNA binding, coactivator recruitment and activation of the estrogen-induced gene GREB1, reflecting a highly interconnected signaling network. In contrast, proliferation driven by dynamic ligands is associated with induction of ERα-mediated transcription in a DNA-binding domain (DBD)-dependent manner. Further, dynamic ligands displayed enhanced anti-inflammatory activity. The DBD-dependent profile was predictive of these signaling patterns in a larger diverse set of natural and synthetic ligands. Thus, ligand dynamics directs unique signaling pathways, and reveals a novel role of the DBD in allosteric control of ERα-mediated signaling.
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The structural basis of direct glucocorticoid-mediated transrepression. Nat Struct Mol Biol 2012; 20:53-8. [PMID: 23222642 PMCID: PMC3539207 DOI: 10.1038/nsmb.2456] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/30/2012] [Indexed: 12/21/2022]
Abstract
A newly discovered negative glucocorticoid response element (nGRE) mediates DNA-dependent transrepression by the glucocorticoid receptor (GR) across the genome and plays a major role in immunosuppressive therapy. The nGRE differs dramatically from activating response elements and the mechanism driving GR binding and transrepression is unknown. To unravel the mechanism of nGRE-mediated transrepression by the glucocorticoid receptor, we characterize the interaction between GR and a nGRE in the thymic stromal lymphopoetin (TSLP) promoter. We show using structural and mechanistic approaches that nGRE binding represents a new mode of sequence recognition by human GR and that nGREs prevent receptor dimerization through a unique GR-binding orientation and strong negative cooperativity, ensuring the presence of monomeric GR at repressive elements.
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Wang YM, Ong SS, Chai SC, Chen T. Role of CAR and PXR in xenobiotic sensing and metabolism. Expert Opin Drug Metab Toxicol 2012; 8:803-17. [PMID: 22554043 DOI: 10.1517/17425255.2012.685237] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The xenobiotic detoxification system, which protects the human body from external chemicals, comprises drug-metabolizing enzymes and transporters whose expressions are regulated by pregnane X receptor (PXR) and the constitutive androstane receptor (CAR). The progress made in a large number of recent studies calls for a timely review to summarize and highlight these key discoveries. AREAS COVERED This review summarizes recent advances in elucidating the roles of PXR and CAR in the xenobiotic detoxification system. It also highlights the progress in understanding the regulation of PXR and CAR activity at the post-translational levels, as well as the structural basis for the regulation of these two xenobiotic sensors. EXPERT OPINION Future efforts are needed to discover novel agonists and antagonists with species and isoform selectivity, to systematically understand the regulation of PXR and CAR at multiple levels (transcriptional, post-transcriptional and post-translational levels) in response to xenobiotics exposure, and to solve the structures of the full-length receptors, which will be enabled by improved protein expression and purification techniques and approaches. In addition, more efforts will be needed to validate PXR and CAR as disease-related therapeutic targets and thus expand their roles as master xenobiotic sensors.
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Affiliation(s)
- Yue-Ming Wang
- St. Jude Children's Research Hospital, Department of Chemical Biology and Therapeutics, 262 Danny Thomas Place, Memphis, TN 38105, USA
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